[gmx-users] RE: SIMPLE QUESTION

[Spiwok Vojtech]

>From: "Raj Badhan" <r.k.badhan at stud.man.ac.uk>
>Organization: University of Manchester
>To: gmx-users at gromacs.org
>Date: Wed, 22 Oct 2003 11:18:42 +0100
>Subject: [gmx-users] SIMPLE QUESTION
>Reply-To: gmx-users at gromacs.org
>
>Dear All,
>I hope someone could answer a simple question for me.
>Simply, how does one know what parameters to input for the 
>rlist/coulombtype/rcoulomb and rvdw of the *.mdp files?
>I hope you could explain this to me, many thanks
>Regards
>
>Mr Raj Badhan
>School of Pharmacy and Pharmacetical Science
>The University of Manchester
>Manchester, UK.
>

Good comparative work is:
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10591101&dopt=Abstract
Study of the electrostatics treatment in molecular dynamics simulations.
Garemyr R, Elofsson A
Proteins. 1999 Nov 15;37(3):417-28.

Generaly:
< 8 A not enough
8 - 20 A depends on application (simple MD, free energy application etc.)
14 - 16 A is my choice for general MD
> 20 A might be a wasting of CPU time

Vojtech Spiwok
ICT Prague
Czech Republic

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